Question: rna-seq fastqc number of parameters to pass
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gravatar for falkjlkdfsnddf
4.3 years ago by
falkjlkdfsnddf0 wrote:

Can i use the RNA seq data, which has passed only a few FASTQC parameters for data analysis.

rna-seq • 1.2k views
ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 4.3 years ago by falkjlkdfsnddf0
1

Err... First, I think you should write again the question and try to explain it in a clearer way. Second, what do you mean by "only a few FASTQC parameters"? Some of the parameters are "more essential" than others depending on your downstream analysis or experiment goal. Of course you can use the data with bad quality.. but, obviously the results  will be affected.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by iraun3.5k

Just to add to what airan said, some of the fastQC tests are meaningless for RNAseq data, while others are important. Without knowing which ones didn't pass and what the associated graphs look like we can't give you any advise.

ADD REPLYlink written 4.3 years ago by Devon Ryan90k

Perhaps you want to read fastqc documentation here (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and choose yourself the parameters. It is explained in a very easy and clear way. Furthermore, there are nice examples of good and bad quality data. If I needed to choose "most important" parameter to pass, I would go for "Overrepresented sequences" and "Per base sequence quality". But I repeat, this depends strongly on your data, your experiment, your downstream analysis...

ADD REPLYlink written 4.3 years ago by iraun3.5k
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